Variant report

Variant	rs12538961
Chromosome Location	chr7:65768032-65768033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:65767632..65769352-chr7:65774697..65777557,2	K562	blood:
2	chr7:65765329..65768039-chr7:65770464..65772414,2	K562	blood:
3	chr7:65761628..65763659-chr7:65767001..65768634,2	K562	blood:

Extended variants
information (count: 132 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs12530506	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530746	1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12530898	1.00[AFR][1000 genomes]
rs12531900	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12532060	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532173	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532182	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532247	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532249	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532278	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532327	1.00[AFR][1000 genomes]
rs12532383	1.00[EUR][1000 genomes]
rs12532423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12532657	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12532675	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12533387	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12533877	1.00[EUR][1000 genomes]
rs12534039	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12534109	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12534249	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12534263	0.97[EUR][1000 genomes]
rs12534477	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12534881	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12535985	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12536816	0.89[EUR][1000 genomes]
rs12536818	1.00[EUR][1000 genomes]
rs12537039	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12537368	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12537698	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12537936	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12538011	0.97[EUR][1000 genomes]
rs12538025	1.00[AFR][1000 genomes]
rs12538113	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12538147	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12538379	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12538686	0.92[EUR][1000 genomes]
rs12539795	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12540667	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12540888	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1363056	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2292936	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs2292937	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs35910256	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3735145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3735146	1.00[EUR][1000 genomes]
rs3735150	1.00[EUR][1000 genomes]
rs3815684	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4149467	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4717291	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4718342	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718345	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718347	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718350	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718353	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718354	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465362	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465363	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465364	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465365	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465367	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62465372	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465373	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465376	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465377	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465380	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62465389	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465390	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465391	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465392	1.00[EUR][1000 genomes]
rs62465394	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465395	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465396	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465397	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465399	0.92[EUR][1000 genomes]
rs62465400	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465401	1.00[EUR][1000 genomes]
rs62465402	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465403	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465404	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62465405	0.92[EUR][1000 genomes]
rs62465422	1.00[EUR][1000 genomes]
rs62465424	1.00[EUR][1000 genomes]
rs62465425	1.00[EUR][1000 genomes]
rs62465426	0.97[EUR][1000 genomes]
rs62465427	0.81[EUR][1000 genomes]
rs62465428	1.00[EUR][1000 genomes]
rs62465429	1.00[EUR][1000 genomes]
rs62465431	1.00[EUR][1000 genomes]
rs62465432	0.97[EUR][1000 genomes]
rs62465474	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62465475	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs62465476	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs62465483	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs62465484	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465512	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465513	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465515	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465519	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465521	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465522	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465525	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465526	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs62465527	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465542	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465545	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62465546	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62465547	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62465550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs62465552	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62465554	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62467421	1.00[AFR][1000 genomes]
rs62467437	1.00[AFR][1000 genomes]
rs62467450	1.00[AFR][1000 genomes]
rs62468669	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468673	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62468679	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62468696	1.00[EUR][1000 genomes]
rs62468699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62468700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62468702	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62468705	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468707	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468708	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62468709	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62468711	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62468712	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12538961	RABGEF1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65761000-65768600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:65761600-65772400	Weak transcription	HSMM	muscle
3	chr7:65762600-65768800	Weak transcription	NHLF	lung
4	chr7:65763000-65768200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr7:65763000-65769200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr7:65763000-65770400	Weak transcription	HepG2	liver
7	chr7:65763000-65786200	Weak transcription	Primary B cells from cord blood	blood
8	chr7:65763200-65768200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr7:65763200-65768200	Weak transcription	NHEK	skin
10	chr7:65763200-65768800	Weak transcription	HMEC	breast
11	chr7:65763800-65769400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:65765800-65768800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr7:65766200-65768200	Enhancers	iPS-20b Cell Line	embryonic stem cell
14	chr7:65766400-65768200	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr7:65766400-65777600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr7:65766600-65768200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr7:65766800-65769800	Enhancers	Fetal Lung	lung
18	chr7:65766800-65780200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr7:65767000-65768200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr7:65767200-65768800	Weak transcription	Stomach Mucosa	stomach
21	chr7:65767400-65768200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr7:65767400-65768200	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr7:65767400-65768200	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr7:65767400-65769800	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr7:65767600-65768200	Enhancers	HUES64 Cell Line	embryonic stem cell
26	chr7:65767600-65769600	Enhancers	Colon Smooth Muscle	Colon
27	chr7:65767800-65768200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr7:65767800-65768400	Enhancers	Fetal Kidney	kidney
29	chr7:65767800-65770200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr7:65767800-65770600	Weak transcription	Ovary	ovary
31	chr7:65767800-65772600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr7:65768000-65769000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr7:65768000-65769000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr7:65768000-65769400	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr7:65768000-65780200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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